deseq2_contrasts: Apply DESeq2's DESeq, results, and lfcShrink to one or more...
In jdreyf/jdcbioinfo: Joslin Diabetes Center bioinformatics utilities

deseq2_contrasts

R Documentation

Apply DESeq2's DESeq, results, and lfcShrink to one or more contrasts, and return a data.frame

Description

Apply DESeq2's DESeq, results,and lfcShrink to one or more contrasts, and return a data.frame

Usage

deseq2_contrasts(
  dds,
  grp = NULL,
  contrast.v,
  add.means = !is.null(grp),
  cols = c("pvalue", "padj", "log2FoldChange"),
  ncore = 1,
  shrunken = TRUE
)

Arguments

`dds`	DESeqDataSet object.
`grp`	Vector of sample groups. These must be valid variable names in R and the same length as `ncol(object)`.
`contrast.v`	Named vector of contrasts, passed to `makeContrasts`.
`add.means`	Logical indicating if (unweighted) group means per row should be added to the output.
`cols`	Columns of `topTable` output to include. Possibilities include `"logFC", "AveExpr", "z", "t", "P.Value", "adj.P.Val", "B"`. Some of these column names are then changed here. If `logFC` is specified, `FC` will automatically also be given.
`ncore`	Number of cores to use.
`shrunken`	logical, whether to shrink the log fold-change